Current Methods of microRNA Analysis

Česká verzia

Authors: Bartošík Martin; Jiráková Ludmila
Authors place of work: Regionální centrum aplikované molekulární onkologie, Masarykův onkologický ústav, Brno
Published in the journal: Klin Onkol 2018; 31(Supplementum 2): 93-101
Category: Review
doi: https://doi.org/10.14735/amko20182S93

Summary

Background:

MicroRNA (miRNA) are a class of short non-coding RNA molecules that regulate gene expression at the post-transcription level by binding to mRNA. By affecting many physiological processes, including cellular proliferation, differentiation, and apoptosis, they have a major impact on the development of cancer as well as other diseases. Hence, miRNAs could serve as potential tumor biomarkers in e.g. early diagnostics, predicting responses to therapy, monitoring relapse, and molecular classification of tumors.

Aim:

miRNA detection requires various sophisticated strategies due to the small size, sequence similarity among family members, and often very low levels of miRNAs in analyzed samples. This review describes standard techniques of miRNA detection, such as the reverse transcriptase polymerase chain reaction, microarrays, and next-generation sequencing, and compares several commercially available detection kits. Major emphasis is given to newly developed technologies and methods, which could make the analysis cheaper and quicker. We present, for instance, alternative amplification techniques (isothermal amplification and the hybridization chain reaction), different types of nanomaterials, special proteins used in miRNA analysis, and a number of biosensors utilizing optical or electrochemical detection.

Conclusion:

The importance of miRNA has led to a huge increase in the number of new methods. Most of them, however, have not been tested on clinical material, and thus it is difficult to assess their potential usefulness in routine practice. Their commercial application strongly depends on strict validation with standard techniques using not only model systems, but also clinical samples.

Key words:

microRNA – gene expression regulation – tumour biomarkers – reverse transcription PCR – biosensors

This work was supported by MEYS – NPS I – LO1413 and GAČR 17-08971S.

The authors declare they have no potential conflicts of interest concerning drugs, products, or services used in the study.

The Editorial Board declares that the manuscript met the ICMJE recommendation for biomedical papers.

Accepted: 9. 7. 2018

Zdroje

1. Huang Y, Shen XJ, Zou Q et al. Biological functions of microRNAs: a review. J Physiol Biochem 2011; 67 (1): 129–139. doi: 10.1007/s13105-010-0050-6.

2. Lee RC, Feinbaum RL, Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 1993; 75 (5): 843–854.

3. miRBase. miRBase: the microRNA database. [online]. Available from: http: //mirbase.org.

4. Calin GA, Dumitru CD, Shimizu M et al. Frequent deletions and down-regulation of micro-RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc Nat Acad Sci USA 2002; 99 (24): 15524–15529. doi: 10.1073/pnas.242606799.

5. Didiano D, Hobert O. Molecular architecture of a miRNA-regulated 3 ‚ UTR. RNA 2008; 14 (7): 1297–1317. doi: 10.1261/rna.1082708.

6. Bartel DP. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 2004; 116 (2): 281–297.

7. Lee H, Han S, Kwon CS et al. Biogenesis and regulation of the let-7 miRNAs and their functional implications. Protein Cell 2016; 7 (2): 100–113. doi: 10.1007/s13238-015-0212-y.

8. Riffo-Campos AL, Riquelme I, Brebi-Mieville P. Tools for sequence-based miRNA target prediction: what to choose? Int J Mol Sci 2016; 17 (12): pii: E1987. doi: 10.3390/ijms17121987.

9. microRNA. Predicted microRNA targets & target downregulation scores. [online]. Available from: http: //34.236.212.39/microrna/home.do.

10. TargetScan. Predicted microRNA targets. [online]. Available from: http: //www.targetscan.org/vert_72/.

11. miRWalk. The miRWalk database. [online]. Available from: http: //mirwalk.umm.uni-heidelberg.de/.

12. miRDB. miRDB target prediction. [online]. Available from: http: //www.mirdb.org/.

13. Slabý O, Svoboda M (ed). MikroRNA v onkologii. 1. vydání. Praha: Galén 2012.

14. Rupaimoole R, Slack FJ. MicroRNA therapeutics: towards a new era for the management of cancer and other diseases. Nat Rev Drug Discov 2017; 16 (3): 203–221. doi: 10.1038/nrd.2016.246.

15. Feng YH, Tsao CJ. Emerging role of microRNA-21 in cancer. Biomed Rep 2016; 5 (4): 395–402. doi: 10.3892/br.2016.747.

16. Hatley ME, Patrick DM, Garcia MR et al. Modulation of K-ras-dependent lung tumorigenesis by microRNA-21. Cancer Cell 2010; 18 (3): 282–293. doi: 10.1016/j.ccr.2010.08.013.

17. Slabý O (ed). MicroRNAs in solid cancer: from biomarkers to therapeutic targets. New York: Nova Science Publishers 2012.

18. Gounaris-Shannon S, Chevassut T. The role of miRNA in haematological malignancy. Bone Marrow Res 2013; 2013: 269107. doi: 10.1155/2013/269107.

19. Calin GA, Croce CM. Chromosomal rearrangements and microRNAs: a new cancer link with clinical implications. J Clin Invest 2007; 117 (8): 2059–2066. doi: 10.1172/JCI32577.

20. Wilting SM, van Boerdonk RAA, Henken FE et al. Methylation-mediated silencing and tumour suppressive function of hsa-miR-124 in cervical cancer. Mol Cancer 2010; 9: 167. doi: 10.1186/1476-4598-9-167.

21. Slabý O. MikroRNA vstupují do klinického testování. Klin Onkol 2012; 25 (2): 139–142.

22. Chakraborty C, Sharma AR, Sharma G et al. Therapeutic miRNA and siRNA: moving from bench to clinic as next generation medicine. Mol Ther Nucl Acids 2017; 8: 132–143. doi: 10.1016/j.omtn.2017.06.005.

23. Kamanu TK, Radovanovic A, Archer JA et al. Exploration of miRNA families for hypotheses generation. Sci Rep 2013; 3: 2940. doi: 10.1038/srep02940.

24. Graybill RM, Bailey RC. Emerging biosensing approaches for microRNA analysis. Anal Chem 2016; 88 (1): 431–450. doi: 10.1021/acs.analchem.5b04679.

25. Aryani A, Denecke B. In vitro application of ribonucleases: comparison of the effects on mRNA and miRNA stability. BMC Res Notes 2015; 8: 164. doi: 10.1186/s13104-015-1114-z.

26. de Planell-Saguer M, Rodicio MC. Detection methods for microRNAs in clinic practice. Clin Biochem 2013; 46 (10–11): 869–878. doi: 10.1016/j.clinbiochem.2013.02. 017.

27. Hu Y, Lan W, Miller D. Next-generation sequencing for microRNA expression profile. Meth Mol Biol 2017; 1617: 169–177. doi: 10.1007/978-1-4939-7046-9_12.

28. Kozomara A, Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 2011; 39 (Suppl 1): D152–D157. doi: 10.1093/nar/gkq1027.

29. Geiss GK, Bumgarner RE, Birditt B et al. Direct multiplexed measurement of gene expression with color-coded probe pairs. Nat Biotechnol 2008; 26 (3): 317–325. doi: 10.1038/nbt1385.

30. Juracek J, Peltanova B, Dolezel J et al. Genome-wide identification of urinary cell-free microRNAs for non-invasive detection of bladder cancer. J Cell Mol Med 2018; 22 (3): 2033–2038. doi: 10.1111/jcmm.13487.

31. Kilic T, Erdem A, Ozsoz M et al. microRNA biosensors: opportunities and challenges among conventional and commercially available techniques. Biosens Bioelectron 2018; 99: 525–546. doi: 10.1016/j.bios.2017.08.007.

32. Tian T, Wang J, Zhou X. A review: microRNA detection methods. Org Biomol Chem 2015; 13 (8): 2226–2238. doi: 10.1039/c4ob02104e.

33. Bartošík M, Hrstka R. Bioelectrochemistry of nucleic acids for early cancer diagnostics – analysis of DNA methylation and detection of microRNAs. Rev Anal Chem 2017; 36 (1): 20160022. doi: 10.1515/revac-2016-0022.

34. Bartošík M, Paleček E, Vojtěšek B. Elektrochemická analýza nukleových kyselin, bílkovin a polysacharidů v biomedicíně. Klin Onkol 2014; 27 (Suppl 1): 53–60. doi: 10.14735/amko20141S53.

35. Paleček E, Bartošík M. Electrochemistry of nucleic acids. Chem Rev 2012; 112 (6): 3427–3481. doi: 10.1021/cr200303p.

36. Ciui B, Jambrec D, Sandulescu R et al. Bioelectrochemistry for miRNA detection. Curr Opin Electrochem 2017; 5 (1): 183–192. doi: 10.1016/j.coelec.2017.09.014.

37. Deng R, Zhang K, Li J. Isothermal amplification for microRNA detection: from the test tube to the cell. Acc Chem Res 2017; 50 (4): 1059–1068. doi: 10.1021/acs.accounts.7b00040.

38. Sun Y, Gregory KJ, Chen NG et al. Rapid and direct microRNA quantification by an enzymatic luminescence assay. Anal Biochem 2012; 429 (1): 11–17. doi: 10.1016/j.ab.2012.06.021.

39. Li Y, Liang L, Zhang C-y. Isothermally sensitive detection of serum circulating miRNAs for lung cancer diagnosis. Anal Chem 2013; 85 (23): 11174–11179. doi: 10.1021/ac403462f.

40. Bi S, Yue S, Zhang S. Hybridization chain reaction: a versatile molecular tool for biosensing, bioimaging, and biomedicine. Chem Soc Rev 2017; 46 (14): 4281–4298. doi: 10.1039/c7cs00055c.

41. Miao X, Ning X, Li Z et al. Sensitive detection of miRNA by using hybridization chain reaction coupled with positively charged gold nanoparticles. Sci Rep 2016; 6: 32358. doi: 10.1038/srep32358.

42. Jamali AA, Pourhassan-Moghaddam M, Dolatabadi JE et al. Nanomaterials on the road to microRNA detection with optical and electrochemical nanobiosensors. TrAC Trends Anal Chem 2014; 55: 24–42. doi: 10.1016/j.trac.2013.10.008.

43. Fiammengo R. Can nanotechnology improve cancer diagnosis through miRNA detection? Biomark Med 2017; 11 (1): 69–86. doi: 10.2217/bmm-2016-0195.

44. Su S, Wu Y, Zhu D et al. On-electrode synthesis of shape-controlled hierarchical flower-like gold nanostructures for efficient interfacial DNA assembly and sensitive electrochemical sensing of microRNA. Small 2016; 12 (28): 3794–3801. doi: 10.1002/smll.201601066.

45. Qiu X, Zhang H, Yu H et al. Duplex-specific nuclease-mediated bioanalysis. Trends Biotechnol 2015; 33 (3): 180–188. doi: 10.1016/j.tibtech.2014.12. 008.

46. Shen W, Deng H, Ren Y et al. A real-time colorimetric assay for label-free detection of microRNAs down to subfemtomolar levels. Chem Commun 2013; 49 (43): 4959–4961. doi: 10.1039/c3cc41565a.

47. Ren Y, Deng H, Shen W et al. A Highly sensitive and selective electrochemical biosensor for direct detection of microRNAs in serum. Anal Chem 2013; 85 (9): 4784–4789. doi: 10.1021/ac400583e.

48. Yin BC, Liu YQ, Ye BC. One-step, multiplexed fluorescence detection of microRNAs based on duplex-specific nuclease signal amplification. J Am Chem Soc 2012; 134 (11): 5064–5067. doi: 10.1021/ja300721s.

49. Torrente-Rodriguez RM, Campuzano S, Lopez-Hernandez E et al. Direct determination of miR-21 in total RNA extracted from breast cancer samples using magnetosensing platforms and the p19 viral protein as detector bioreceptor. Electroanalysis 2014; 26 (10): 2080–2087. doi: 10.1002/elan.201400317.

50. Torrente-Rodriguez RM, Campuzano S, Lopez-Hernandez E et al. Simultaneous detection of two breast cancerrelated miRNAs in tumor tissues using p19-based disposable amperometric magnetobiosensing platforms. Biosens Bioelectron 2015; 66: 385–391. doi: 10.1016/j.bios.2014.11.047.

51. Torrente-Rodriguez RM, Ruiz-Valdepenas Montiel V, Campuzano S et al. Fast electrochemical miRNAs determination in cancer cells and tumor tissues with antibody-functionalized magnetic microcarriers. ACS Sensors 2016; 1 (7): 896–903. doi: 10.1021/acssensors.6b00 266.

52. Wang Y, Zheng D, Tan Q et al. Nanopore-based detection of circulating microRNAs in lung cancer patients. Nat Nanotechnol 2011; 6 (10): 668–674. doi: 10.1038/nnano.2011.147.